After managing to capture Cornelia, Lelouch forces her to reveal what little information she knows of Marianne's murder, but the answers do not please him one bit. V.V. takes Nunnally to Kaminejima, and Lelouch abandons the Black Knights to rescue his sister. Without Lelouch, the Black Knights begin to lose ground to the Britannian Army. Suzaku follows Lelouch, leading to a final confrontation between the former friends.

Lelouch successfully escapes with Empress Tianzi and the Black Knights attempt to unite with their Indian allies. Desperate to recover the Empress, the Eunuchs agree to forgive Li Xingke if he rescues her. To that end, he is granted use of the powerful Shenhu. Kallen intercepts him with the Guren Flight-Enabled Version, but its power runs out and she is taken hostage. Lelouch swears to rescue her, despite Diethard Reid's suggestion to retreat. Xingke demonstrates his skill as a strategist, forcing the Black Knights to retreat to a mountainside monument constructed as the tomb for the former Tianzi, hoping the Federation would be hesitant to attack. The Eunuchs turn on Xingke and his troops, having enlisted the aid of the Britannian forces. Meanwhile, another Lelouch is present at the Ashford Academy.

Rolo admits to causing Shirley's death; rather than blame Rolo, Lelouch blames the existence of Geass itself. In retaliation, he mounts an assault on the Geass Directorate, slaughtering every man, woman, and child within the stronghold. V.V. pilots the Siegfried in an effort to stop the Black Knights, but is defeated by both Lelouch and Cornelia. He escapes to the Thought Elevator, where Charles awaits, and when Lelouch follows he is transported to the Sword of Akasha. Meanwhile, Kallen and Nunnally discuss Lelouch. They are interupted by Suzaku, who, despite having been told that Shirley's death was a suicide, decides to interrogate Kallen using Refrain, in order to confirm his suspicion that Lelouch has become Zero again.

Lelouch begins his reformation of Britannia, abolishing the aristocracy and Area system. The Knights of Rounds attempt to remove Lelouch from power, but Suzaku, piloting the Lancelot Albion, easily obliterates their ranks, killing Bismarck Waldstein and two other Rounds members while only disabling Gino's Knightmare. His position secure, Lelouch announces his intention to join the U.F.N. On the way to the meeting, he and Kallen bid each other farewell after she kisses him, Kallen having been unable to get Lelouch to answer any of her questions. When the UFN demands that he accept a limit to his voting power to prevent Britannia from attaining an automatic majority, Lelouch forces their hand by having Suzaku take the U.F.N. leaders hostage and Britannia's military surround Japan. During the commotion, the Britannian capital is obliterated by Schenizel, who is aboard his new flying fortress, the Damocles. He reveals to Lelouch that Nunnally is alive, and she declares herself to be Lelouch and Suzaku's enemy.

Lelouch and Suzaku fight for the sake of their promise, the Zero Requiem. Suzaku battles Kallen, while Lelouch confronts Nunnally, his biggest and dearest enemy.